8BDW

Crystal structure of CnaB2 domain from Lactobacillus plantarum

PDB DOI: https://doi.org/10.2210/pdb8BDW/pdb

Classification: PEPTIDE BINDING PROTEIN
Organism(s): Lactiplantibacillus plantarum
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2022-10-20 Released: 2023-02-22
Deposition Author(s): Taberman, H., Hakanpaa, J., Linder, M.B., Aranko, A.S.
Funding Organization(s): Academy of Finland

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.86 Å
R-Value Free: 0.187
R-Value Work: 0.154

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Biomolecular Click Reactions Using a Minimal pH-Activated Catcher/Tag Pair for Producing Native-Sized Spider-Silk Proteins.

Fan, R., Hakanpaa, J., Elfving, K., Taberman, H., Linder, M.B., Aranko, A.S.

(2023) Angew Chem Int Ed Engl 62: e202216371-e202216371

PubMed: 36695475 Search on PubMed
DOI: https://doi.org/10.1002/anie.202216371
Primary Citation of Related Structures:
8BDW

PubMed Abstract:
A type of protein/peptide pair known as Catcher/Tag pair spontaneously forms an intermolecular isopeptide bond which can be applied for biomolecular click reactions. Covalent protein conjugation using Catcher/Tag pairs has turned out to be a valuable tool in biotechnology and biomedicines, but it is essential to increase the current toolbox of orthogonal Catcher/Tag pairs to expand the range of applications further, for example, for controlled multiple-fragment ligation. We report here the engineering of novel Catcher/Tag pairs for protein ligation, aided by a crystal structure of a minimal CnaB domain from Lactobacillus plantarum. We show that a newly engineered pair, called SilkCatcher/Tag enables efficient pH-inducible protein ligation in addition to being compatible with the widely used SpyCatcher/Tag pair. Finally, we demonstrate the use of the SilkCatcher/Tag pair in the production of native-sized highly repetitive spider-silk-like proteins with >90 % purity, which is not possible by traditional recombinant production methods.

Organizational Affiliation

Department of Bioproducts and Biosystems, School of Chemical Engineering, Aalto University, P.O. Box 16100, 02150, Espoo, Finland.

Macromolecule Content

Total Structure Weight: 123.35 kDa
Atom Count: 10,004
Modelled Residue Count: 1,142
Deposited Residue Count: 1,176
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cell surface adherence protein,collagen-binding domain, LPXTG-motif cell wall anchor	A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	98	Lactiplantibacillus plantarum	Mutation(s): 0 Gene Names: lp_2578
UniProt
Find proteins for F9UR90 (Lactiplantibacillus plantarum (strain ATCC BAA-793 / NCIMB 8826 / WCFS1)) Explore F9UR90 Go to UniProtKB: F9UR90
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	F9UR90
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
TRS Query on TRS Download Ideal Coordinates CCD File SDF format, chain TA [auth L] MOL2 format, chain TA [auth L]	TA [auth L]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C₄ H₁₂ N O₃ LENZDBCJOHFCAS-UHFFFAOYSA-O		Interactions Focus chain TA [auth L] Interactions & Density Focus chain TA [auth L]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain EA [auth G] SDF format, chain KA [auth I] SDF format, chain PA [auth J] SDF format, chain W [auth E] MOL2 format, chain EA [auth G] MOL2 format, chain KA [auth I] MOL2 format, chain PA [auth J] MOL2 format, chain W [auth E]	EA [auth G], KA [auth I], PA [auth J], W [auth E]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain EA [auth G] Focus chain KA [auth I] Focus chain PA [auth J] Focus chain W [auth E] Interactions & Density Focus chain EA [auth G] Focus chain KA [auth I] Focus chain PA [auth J] Focus chain W [auth E]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain AA [auth G] SDF format, chain BA [auth G] SDF format, chain CA [auth G] SDF format, chain DA [auth G] SDF format, chain FA [auth H] SDF format, chain GA [auth H] SDF format, chain HA [auth I] SDF format, chain IA [auth I] SDF format, chain JA [auth I] SDF format, chain LA [auth I] SDF format, chain M [auth A] SDF format, chain MA [auth J] SDF format, chain N [auth A] SDF format, chain NA [auth J] SDF format, chain O [auth B] SDF format, chain OA [auth J] SDF format, chain P [auth C] SDF format, chain Q [auth D] SDF format, chain QA [auth K] SDF format, chain R [auth D] SDF format, chain RA [auth K] SDF format, chain S [auth D] SDF format, chain SA [auth L] SDF format, chain T [auth D] SDF format, chain U [auth E] SDF format, chain UA [auth L] SDF format, chain V [auth E] SDF format, chain VA [auth L] SDF format, chain X [auth F] SDF format, chain Y [auth F] SDF format, chain Z [auth G] MOL2 format, chain AA [auth G] MOL2 format, chain BA [auth G] MOL2 format, chain CA [auth G] MOL2 format, chain DA [auth G] MOL2 format, chain FA [auth H] MOL2 format, chain GA [auth H] MOL2 format, chain HA [auth I] MOL2 format, chain IA [auth I] MOL2 format, chain JA [auth I] MOL2 format, chain LA [auth I] MOL2 format, chain M [auth A] MOL2 format, chain MA [auth J] MOL2 format, chain N [auth A] MOL2 format, chain NA [auth J] MOL2 format, chain O [auth B] MOL2 format, chain OA [auth J] MOL2 format, chain P [auth C] MOL2 format, chain Q [auth D] MOL2 format, chain QA [auth K] MOL2 format, chain R [auth D] MOL2 format, chain RA [auth K] MOL2 format, chain S [auth D] MOL2 format, chain SA [auth L] MOL2 format, chain T [auth D] MOL2 format, chain U [auth E] MOL2 format, chain UA [auth L] MOL2 format, chain V [auth E] MOL2 format, chain VA [auth L] MOL2 format, chain X [auth F] MOL2 format, chain Y [auth F] MOL2 format, chain Z [auth G]	AA [auth G] BA [auth G] CA [auth G] DA [auth G] FA [auth H] AA [auth G], BA [auth G], CA [auth G], DA [auth G], FA [auth H], GA [auth H], HA [auth I], IA [auth I], JA [auth I], LA [auth I], M [auth A], MA [auth J], N [auth A], NA [auth J], O [auth B], OA [auth J], P [auth C], Q [auth D], QA [auth K], R [auth D], RA [auth K], S [auth D], SA [auth L], T [auth D], U [auth E], UA [auth L], V [auth E], VA [auth L], X [auth F], Y [auth F], Z [auth G]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain AA [auth G] Focus chain BA [auth G] Focus chain CA [auth G] Focus chain DA [auth G] Focus chain FA [auth H] Focus chain GA [auth H] Focus chain HA [auth I] Focus chain IA [auth I] Focus chain JA [auth I] Focus chain LA [auth I] Focus chain M [auth A] Focus chain MA [auth J] Focus chain N [auth A] Focus chain NA [auth J] Focus chain O [auth B] Focus chain OA [auth J] Focus chain P [auth C] Focus chain Q [auth D] Focus chain QA [auth K] Focus chain R [auth D] Focus chain RA [auth K] Focus chain S [auth D] Focus chain SA [auth L] Focus chain T [auth D] Focus chain U [auth E] Focus chain UA [auth L] Focus chain V [auth E] Focus chain VA [auth L] Focus chain X [auth F] Focus chain Y [auth F] Focus chain Z [auth G] Interactions & Density Focus chain AA [auth G] Focus chain BA [auth G] Focus chain CA [auth G] Focus chain DA [auth G] Focus chain FA [auth H] Focus chain GA [auth H] Focus chain HA [auth I] Focus chain IA [auth I] Focus chain JA [auth I] Focus chain LA [auth I] Focus chain M [auth A] Focus chain MA [auth J] Focus chain N [auth A] Focus chain NA [auth J] Focus chain O [auth B] Focus chain OA [auth J] Focus chain P [auth C] Focus chain Q [auth D] Focus chain QA [auth K] Focus chain R [auth D] Focus chain RA [auth K] Focus chain S [auth D] Focus chain SA [auth L] Focus chain T [auth D] Focus chain U [auth E] Focus chain UA [auth L] Focus chain V [auth E] Focus chain VA [auth L] Focus chain X [auth F] Focus chain Y [auth F] Focus chain Z [auth G]